Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe
KAUST Grant NumberKUK-C1-013-04
Online Publication Date2013-10-23
Print Publication Date2013-12-01
Permanent link to this recordhttp://hdl.handle.net/10754/598406
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AbstractPolyadenylation of pre-mRNAs, a critical step in eukaryotic gene expression, is mediated by cis elements collectively called the polyadenylation signal. Genome-wide analysis of such polyadenylation signals was missing in fission yeast, even though it is an important model organism. We demonstrate that the canonical AATAAA motif is the most frequent and functional polyadenylation signal in Schizosaccharomyces pombe. Using analysis of RNA-Seq data sets from cells grown under various physiological conditions, we identify 3' UTRs for nearly 90% of the yeast genes. Heterogeneity of cleavage sites is common, as is alternative polyadenylation within and between conditions. We validated the computationally identified sequence elements likely to promote polyadenylation by functional assays, including qRT-PCR and 3'RACE analysis. The biological importance of the AATAAA motif is underlined by functional analysis of the genes containing it. Furthermore, it has been shown that convergent genes require trans elements, like cohesin for efficient transcription termination. Here we show that convergent genes lacking cohesin (on chromosome 2) are generally associated with longer overlapping mRNA transcripts. Our bioinformatic and experimental genome-wide results are summarized and can be accessed and customized in a user-friendly database Pomb(A).
CitationSchlackow M, Marguerat S, Proudfoot NJ, Bahler J, Erban R, et al. (2013) Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe. RNA 19: 1617–1631. Available: http://dx.doi.org/10.1261/rna.040675.113.
SponsorsWe thank Konrad Krawczyk for valuable advice and support. This work was supported in part by the King Abdullah University of Science and Technology (KAUST) (KUK-C1-013-04); the Engineering and Physical Sciences Research Council (to M. S.); the L'Oreal/UNESCO Woman in Science UK and Ireland award (to M. G.), the MRC Career Development Award (to M. G.); the Wellcome Trust Senior Investigator Award (to J.B.), the Wellcome Trust programme grant (to N.J.P.), and the European Research Council grant agreement (239870 to R. E.); Royal Society for a University Research Fellowship; Brasenose College, University of Oxford (to R. E.); a Nicholas Kurti Junior Fellowship (to R. E.); and the Leverhulme Trust Philip Leverhulme Prize (to R.E.).
PublisherCold Spring Harbor Laboratory
PubMed Central IDPMC3884648
CollectionsPublications Acknowledging KAUST Support
- Genome-wide mapping of polyadenylation sites in fission yeast reveals widespread alternative polyadenylation.
- Authors: Mata J
- Issue date: 2013 Aug
- Homologous mRNA 3' end formation in fission and budding yeast.
- Authors: Humphrey T, Sadhale P, Platt T, Proudfoot N
- Issue date: 1991 Nov
- Nascent transcription from the nmt1 and nmt2 genes of Schizosaccharomyces pombe overlaps neighbouring genes.
- Authors: Hansen K, Birse CE, Proudfoot NJ
- Issue date: 1998 Jun 1
- Poly(A) site choice during mRNA 3'-end formation in the Schizosaccharomyces pombe wos2 gene.
- Authors: Muñoz MJ, Daga RR, Garzón A, Thode G, Jimenez J
- Issue date: 2002 Aug
- Comparative analysis of alternative polyadenylation in <i>S. cerevisiae</i> and <i>S. pombe</i>.
- Authors: Liu X, Hoque M, Larochelle M, Lemay JF, Yurko N, Manley JL, Bachand F, Tian B
- Issue date: 2017 Oct